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Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies
2012
PLoS Computational Biology
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The evolution of enzyme function in the isomerases. ...
With completely sequenced genomes, the full complement of enzymes in an organism can be defined, and 3D structures have been determined for many enzyme families. ...
We have adopted a number of approaches to define the functional impact of these mutations on myosin function. ...
doi:10.1371/journal.pcbi.1002403
pmid:22396634
pmcid:PMC3291543
fatcat:77jw2t4jjbgarjsgexccje34iy
FunTree: advances in a resource for exploring and contextualising protein function evolution
2015
Nucleic Acids Research
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This allows the investigation of how novel functions have evolved within a structurally defined superfamily and provides a means to analyse trends across many superfamilies. ...
This is done not only within the context of a protein's sequence and structure but also the relationships of their functions. ...
Christine Orengo for useful comments and suggestions as well as the European Bioinformatics Institute for the use of their highperformance computing cluster in processing the data. ...
doi:10.1093/nar/gkv1274
pmid:26590404
pmcid:PMC4702901
fatcat:qnfbhibpjfapfd3kanbp6nqcx4
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies
2016
Journal of Molecular Biology
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Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, ...
Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. ...
Fig. 4 . 4 Summary of top 10 bond types that are gained and lost through the evolution of enzyme function within 379 domain superfamilies. ...
doi:10.1016/j.jmb.2015.11.010
pmid:26585402
pmcid:PMC4751976
fatcat:rqkj2aj7nrbhzngzy7q3sppquq
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies
2011
Nucleic Acids Research
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Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to ...
This is done not only within the context of an enzyme's sequence and structure but also the relationships of their reactions. ...
Bringing together this range of data into a single resource allows the investigation of the evolution of novel enzyme functions within structurally defined superfamilies. ...
doi:10.1093/nar/gkr852
pmid:22006843
pmcid:PMC3245072
fatcat:lwlpp7cazvdy5ebfxequzzujnu
Exploring the structure and function paradigm
2008
Current Opinion in Structural Biology
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Many of these structures are novel -using the 5Å threshold defined above for fold similarity). ...
A detailed analysis of limited sets of superfamilies recently culminated in the development of a new resource for the study of structure-function relationships within enzyme superfamilies, namely the Structure ...
doi:10.1016/j.sbi.2008.05.007
pmid:18554899
pmcid:PMC2561214
fatcat:ds3bhbjjqjf3ljcroed3uonc4e
New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships
2014
Journal of Biological Chemistry
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Comparison among all of the sequences and/or structures in a superfamily can then be used to deduce how evolution has varied these features to produce new enzyme functions from the ancestral structural ...
We illustrate here some major themes emerging from large scale studies of functionally diverse enzyme superfamilies that impact our understanding of the evolution of enzyme function. ...
The concept of moonlighting enzymes, describing additional structural or regulatory functions performed in addition to their catalytic functions, has also provided novel insight about the evolution of ...
doi:10.1074/jbc.r114.569350
pmid:25210038
pmcid:PMC4215206
fatcat:biiui2rljngshklchfp6465hom
MANET: tracing evolution of protein architecture in metabolic networks
2006
BMC Bioinformatics
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depicting the evolution of protein fold architecture. ...
Our aim is to find evolutionary patterns and processes embedded in the architecture and function of modern metabolism, using information derived from structural genomics. ...
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies. ...
doi:10.1186/1471-2105-7-351
pmid:16854231
pmcid:PMC1559654
fatcat:vdp6uhww7jau3nkczazhlfcnsy
Evolutionary Origin of a Secondary Structure: π-Helices as Cryptic but Widespread Insertional Variations of α-Helices That Enhance Protein Functionality
2010
Journal of Molecular Biology
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This new understanding of π-helices paves the way for this generally overlooked motif to become a noteworthy feature that will aid tracing the evolution of many protein families, guide investigations of ...
a "missing link" intermediary form of the ribonucleotide reductase family, vestigial π-helices, and a novel function for π-helices we term peristaltic-like shifts. ...
Acknowledgments We thank Joe Thornton, Jacque Fetrow and Brian Matthews for critique of an earlier manuscript. ...
doi:10.1016/j.jmb.2010.09.034
pmid:20888342
pmcid:PMC2981643
fatcat:777cruvrgzb5xamctplnlg56e4
New computational approaches to understanding molecular protein function
2018
PLoS Computational Biology
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functions within a protein superfamily-that is, the number of clusters that captures biologically relevant functional boundaries that correlate with the level of molecular functional hierarchy being pursued ...
The Structure-Function Linkage Database (SFLD) also defines a molecular functional hierarchy, in this case as superfamily, subgroup, and family (Fig 1) [26]. ...
doi:10.1371/journal.pcbi.1005756
pmid:29621256
pmcid:PMC5886384
fatcat:5f3gv2hx25awlfaod3thv67j5u
Understanding enzyme function evolution from a computational perspective
2017
Current Opinion in Structural Biology
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In this review, we will explore recent computational approaches to understand enzyme evolution from the perspective of protein structure, dynamics and promiscuity. ...
We will present quantitative methods to measure the size of evolutionary steps within a structural domain, allowing the correlation between change in substrate and domain structure to be assessed, and ...
A review of integrative approaches to explore enzyme evolution and functional diversity within enzyme superfamilies, highlighting recent large-scale experimental methods to determine activity profiles ...
doi:10.1016/j.sbi.2017.08.003
pmid:28892668
fatcat:ph7tbjfqevdqhiai4dkuwmygmy
Proteins with Class α/β Fold Have High-level Participation in Fusion Events
2002
Journal of Molecular Biology
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An exhaustive survey of fusion events within 30 completely sequenced genomes and subsequent structure annotations to the component proteins at a SCOP superfamily level with hidden Markov models was carried ...
Here, we took a new approach to the analysis of the structural features of the proteins involved in fusion events. ...
This work was funded by the National Natural Science Grant in China (no. 39980007) and the National Key Foundational Research Grant in China (985, 863). ...
doi:10.1016/s0022-2836(02)00467-9
pmid:12095249
fatcat:vjr5sn3agzhdrg6yv2onulsvda
The history of the CATH structural classification of protein domains
2015
Biochimie
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The establishment of comprehensive function annotation resources has also meant that domain families can be functionally annotated allowing insights into functional divergence and evolution within protein ...
We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their ...
too, allowing large scale studies of the divergence of function within superfamilies during evolution. ...
doi:10.1016/j.biochi.2015.08.004
pmid:26253692
pmcid:PMC4678953
fatcat:jb7v7o2f3fc37fjoc2lopkcy44
Functional innovation from changes in protein domains and their combinations
2016
Current Opinion in Structural Biology
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Domains are the functional building blocks of proteins. In this work we discuss how domains can contribute to the evolution of new functions. ...
Domains themselves can evolve through various mechanisms, altering their intrinsic function. Domains can also facilitate functional innovations by combining with other domains to make novel proteins. ...
Domain insertions can act to drive the evolution of new functions such as in the large structurally and functionally diverse HADSF enzyme superfamily (Huang et al. 2015) , here different levels of promiscuity ...
doi:10.1016/j.sbi.2016.05.016
pmid:27309309
fatcat:vykx2i6uabfazpwv4oozsyxnle
Leveraging Enzyme Structure−Function Relationships for Functional Inference and Experimental Design: The Structure−Function Linkage Database†
2006
Biochemistry
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We present the results of analyses using the SFLD in correcting misannotations, guiding protein engineering experiments, and elucidating the function of recently solved enzyme structures from the structural ...
residuesshelps elucidate the structure-function relationships of enzymes. ...
Enzyme functional domains are defined in the SFLD as the functional domains of individual enzymatic proteins. ...
doi:10.1021/bi052101l
pmid:16489747
fatcat:dajbxfc4ajbq3hckmbou2ep2v4
Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies
2020
Nucleic Acids Research
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functions within a shared 3D-structure of the superfamily, determine common and specific patterns of function-associated local structural elements, assist to select hot-spots for rational design and to ...
Zebra2 is a highly automated web-tool to search for subfamily-specific and conserved positions (i.e. the determinants of functional diversity as well as the key catalytic and structural residues) in protein ...
ACKNOWLEDGEMENTS The use of HPC computing resources at the Lomonosov Moscow State University supported by the project RFMEFI62117X0011 to prepare the PDB and UniProt databases in a format compatible with ...
doi:10.1093/nar/gkaa276
pmid:32313959
fatcat:3gmxnpwn6zapvhiwiipk7scfay
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